Have you planned for the routing in the USB3 interface? For detailed recommendations for proper USB3 SERDES signal connection and routing, see the High-Speed Interface Layout Guidelines Application Report. Add appropriate constraints or routing requirements to your schematic. This will vary from tool to tool.
Have you connected the correct SERDES pairs for USB3 operation? The AM65x includes two SERDES transmit and receive pairs named SERDES0 and SERDES1. Each can support a number of SERDES interfaces, but the correct SERDES interface must be used for some functions. USB3 is only supported using the SERDES0 transmit and receive signals.
Have you included DC-blocking capacitors in the correct location? DC-blocking capacitors are required for USB3 transmit and receive pairs, but the capacitors should be placed closer to the USB3 transmitter. If a USB3 connector is used in the design, the receive pair will be connected directly to the connector. The DC-blocking caps for the receive pair are present on the device connected to the USB3 connector.
Have you connected the correct USB2 signals for the USB2 compatibility? USB3 connectors include both the USB3 and USB2 connections for compatibility with older USB devices. The AM65x supports two USB2 interfaces, but the USB0_DM/P signals should be connected to a USB3 connector. USB1_DM/P is a USB2-only interface.